In Windows Server 2003 to 2012 R2 the SSL / TLS protocols are controlled by flags in the registry set at HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\Schannel\Protocols.

To disable SSLv3, which the POODLE vulnerability is concerned with, create a subkey at the above location (if it's not already present) named SSL 3.0 and, under that, a subkey named Server (if it's not already present). At this location (HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\Schannel\Protocols\SSL 3.0\Server) create a DWORD value named Enabled and leave it set at 0.

Disabling SSL 2.0, which you should also be doing, is done the same way, except that you'll be using a key named SSL 2.0 in the above registry path.